I think the system is pretty good for two reasons. (1) It works very well at selecting the top teams. (Top teams in November, not in September.) (2) Every team controls their own destiny. If they qualify, they earned their way in at regionals and over the course of the season. If they didn't qualify, they almost always just didn't get it done when they needed to.
One knock is that auto qualifiers from bad regions can be worse than teams in tough regions who didn't make it. I agree it can happen, but I don't think it's a huge problem. First, I think it's healthy for the sport to have representation from all over the country. It maybe helps even things out in the long run by spreading talent, recruiting, and interest in the sport a bit more broadly. Second, picking the 25-31st best teams correctly is only so important. Third, if you look at historical results, it's not like those teams getting dead last every year. They usually run like they belong at the meet.
I also think the regionals are good, competitive meets that are good for the sport including the teams finishing in the middle and back who use it as an end-of-season event to stack up against the best in the region. Also, sometimes an unexpected school like Bradley will get really good and make nationals. You don't have to do anything special with your schedule or convince a committee. Just run the same meets you run every year, but faster.